7M8W: Prostaglandin D2 receptor 2, Endolysin chimera

XFEL crystal structure of the prostaglandin D2 receptor CRTH2 in complex with 15R-methyl-PGD2. Determined by X-ray diffraction at 2.61 Å resolution. Released 25 Aug 2021.

Method: X-ray diffraction
Resolution: 2.61 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 1
Atoms: 3,501
Mol. weight: 53.29 kDa
Ligands: FLC, YSS
Released: 25 Aug 2021

Explore 7M8W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M8W contains 23 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-19	8
α-helix	33-59	27
α-helix	65-92	28
α-helix	102-134	33
α-helix	136-142	7
α-helix	145-162	18
α-helix	164-168	5
β-strand	170-174	5	1
β-strand	180-184	5	1
α-helix	186-188	3
α-helix	195-211	17
α-helix	212-216	5
α-helix	217-903	24
α-helix	1071-1080	10
α-helix	1085-1089	5
α-helix	1093-1111	19
α-helix	1115-1122	8
α-helix	1126-1134	9
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	1159-1161	3
α-helix	240-242	3
α-helix	245-272	28
α-helix	278-306	29
α-helix	309-324	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin D2 receptor 2, Endolysin chimera	A	protein	470	Homo sapiens, Enterobacteria phage T4	D9IEF7, Q9Y5Y4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7M8W_1 Prostaglandin D2 receptor 2, Endolysin chimera (chains A)
GMSANATLKPLCPILEQMSRLQSHSATSIRYIDHAAVLLHGLASLLGLVENGVILFVVGC
RMRQTVVTTWVLHLALSDLLASASLPFFTYFLAVGHSWELGTTFCKLHSSIFFLNMFASG
FLLSAISLDRCLQVVRPVWAQNHRTVAAAHKVCLVLWALAVLNTVPYFVFRDTISRLDGR
IMCYYNVLLLNPGPDRDATCNSRQAALAVSKFLLAFLVPLAIIASSHAAVSLRLQHRADL
GLQHRNIFEMLRIDEGGGSGGDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL
INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWD
AYRRRPGRFVRLVAAVVAAFALCWGPYHVFSLLEARAHANPGLRPLVWRGLPFVTSLAFF
NSVANPVLYVLTCPDMLRKLRRSLRTVLESVLVDDSELGGAGSSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	1
YSS	15R-methyl-prostaglandin D2	C21 H34 O5	1

Water and common crystallization additives (SO4, NA) are not listed.

Primary citation

Molecular basis for lipid recognition by the prostaglandin D 2 receptor CRTH2. Liu, H., Deepak, R.N.V.K., Shiriaeva, A. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2102813118 · PubMed

Other PDB entries of the same protein (UniProt D9IEF7), best resolution first:

7LOG 0.99 Å, T4 lysozyme mutant L99A in complex with 3-butylpyridine
9DJK 1.04 Å, T4 Lysozyme D127H/V131H
7XE7 1.05 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH10
7LXA 1.07 Å, T4 lysozyme mutant L99A
9DJM 1.08 Å, T4 Lysozyme K147H/T151H
7XE6 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7
7XEA 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking
9DJI 1.1 Å, T4 Lysozyme R119H/Q123H
9DJD 1.11 Å, T4 Lysozyme A73H/G77H/Y139F co-crystallized with Cu(II)-NTA
8F11 1.12 Å, T4 lysozyme with a 2,6-diazaadamantane nitroxide (DZD) spin label
9DJB 1.13 Å, T4 Lysozyme A73H/G77H
9DJC 1.13 Å, T4 Lysozyme A73H/G77H/Y139F

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